Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2520
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22723
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:4778 original size:27 final size:27
Alignment explanation
Indices: 4761--4938 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
4751 ATATTAAGTC
4761 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
4788 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
4816 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *** ** *
4843 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
4870 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
4897 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
4924 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
4939 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 104 0.79
28 27 0.21
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:4900 original size:54 final size:54
Alignment explanation
Indices: 4761--4937 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
4751 ATATTAAGTC
* * *
4761 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAA-T
* ** * *
4816 CGCACACTTAGTGC-TACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
4870 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
4924 CGCACACTTAGTGC
1 CGCACACTTAGTGC
4938 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 44 0.42
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:4927 original size:81 final size:82
Alignment explanation
Indices: 4782--4937 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
4772 TGCTATATAA
* *
4782 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
4847 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
4864 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
4927 ACACTTAGTGC
65 ACACTTAGTGC
4938 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:8790 original size:34 final size:35
Alignment explanation
Indices: 8744--8826 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
8734 TTGAACAATC
* *** *
8744 TGGGCTTAAGCCCATAT-CAGTCGTAATATTAGTG
1 TGGGCTTTAGCCCATATACAGTAACAATATTAATG
*
8778 TGGGCTTTAGCCCA-ATACAGTAACAGTATTAATG
1 TGGGCTTTAGCCCATATACAGTAACAATATTAATG
*
8812 TGGGCCTTAGCCCAT
1 TGGGCTTTAGCCCAT
8827 TTCGGTACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 2 0.05
34 38 0.95
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (35 bp):
TGGGCTTTAGCCCATATACAGTAACAATATTAATG
Found at i:15247 original size:13 final size:13
Alignment explanation
Indices: 15229--15254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15219 GCCATCAGCA
15229 CCGTGATTCCAGG
1 CCGTGATTCCAGG
15242 CCGTGATTCCAGG
1 CCGTGATTCCAGG
15255 TTTCGAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
CCGTGATTCCAGG
Found at i:17194 original size:39 final size:40
Alignment explanation
Indices: 17045--17308 Score: 340
Period size: 40 Copynumber: 6.7 Consensus size: 40
17035 GCTACTAGTT
* * *
17045 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
17085 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17125 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17165 CAAATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
17204 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
17243 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
17284 CAAA-GCCTGCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
17309 CATCATTCGA
Statistics
Matches: 204, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.01
39 72 0.35
40 117 0.57
41 13 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:18494 original size:50 final size:51
Alignment explanation
Indices: 18438--18584 Score: 233
Period size: 56 Copynumber: 2.8 Consensus size: 51
18428 TAGTTTATTG
18438 CCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTT-ATGTTTTGC
1 CCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTAATGTTTTGC
18488 CCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGC
1 CCATGCTTCTTATTTTATTCTTCCATTAACACAACATG-TT--T-A-ATGTTTTGC
*
18544 CCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTT
1 CCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTT
18585 CATGACATGT
Statistics
Matches: 90, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
50 38 0.42
51 2 0.02
53 2 0.02
55 2 0.02
56 46 0.51
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.47
Consensus pattern (51 bp):
CCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTAATGTTTTGC
Found at i:18546 original size:56 final size:56
Alignment explanation
Indices: 18479--18603 Score: 241
Period size: 56 Copynumber: 2.2 Consensus size: 56
18469 CAACATGTTT
18479 ATGTTTTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGAC
1 ATGTTTTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGAC
*
18535 ATGTTTTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGAC
1 ATGTTTTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGAC
18591 ATGTTTTGCCCAT
1 ATGTTTTGCCCAT
18604 CATCCCTTGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (56 bp):
ATGTTTTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGAC
Done.